Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_diversity_mantel.xml @ 0:370e0b6e9826 draft
Uploaded
| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | 914fa4daf16a |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:370e0b6e9826 |
|---|---|
| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.4"> | |
| 3 <description> - Apply the Mantel test to two distance matrices</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime diversity mantel | |
| 9 | |
| 10 --i-dm1=$idm1 | |
| 11 --i-dm2=$idm2 | |
| 12 | |
| 13 #if str($pmethod) != 'None': | |
| 14 --p-method=$pmethod | |
| 15 #end if | |
| 16 | |
| 17 #if $ppermutations: | |
| 18 --p-permutations=$ppermutations | |
| 19 #end if | |
| 20 | |
| 21 #if $pintersectids: | |
| 22 --p-intersect-ids | |
| 23 #end if | |
| 24 | |
| 25 #if str($plabel1): | |
| 26 --p-label1="$plabel1" | |
| 27 #end if | |
| 28 | |
| 29 #if str($plabel2): | |
| 30 --p-label2="$plabel2" | |
| 31 #end if | |
| 32 | |
| 33 --o-visualization=ovisualization | |
| 34 ; | |
| 35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
| 36 && cp -r out/* '$ovisualization.files_path' | |
| 37 && mv '$ovisualization.files_path/index.html' '$ovisualization'; | |
| 38 ]]></command> | |
| 39 <inputs> | |
| 40 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data"/> | |
| 41 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data"/> | |
| 42 <param label="--p-method: " name="pmethod" optional="True" type="select"> | |
| 43 <option selected="True" value="None">Selection is Optional</option> | |
| 44 <option value="spearman">spearman</option> | |
| 45 <option value="pearson">pearson</option> | |
| 46 </param> | |
| 47 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/> | |
| 48 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/> | |
| 49 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="'Distance Matrix 1'"/> | |
| 50 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="'Distance Matrix 2'"/> | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 54 </outputs> | |
| 55 <help><![CDATA[ | |
| 56 Apply the Mantel test to two distance matrices | |
| 57 ############################################## | |
| 58 | |
| 59 Apply a two-sided Mantel test to identify correlation between two distance | |
| 60 matrices. Note: the directionality of the comparison has no bearing on the | |
| 61 results. Thus, comparing distance matrix X to distance matrix Y is | |
| 62 equivalent to comparing Y to X. Note: the order of samples within the two | |
| 63 distance matrices does not need to be the same; the distance matrices will | |
| 64 be reordered before applying the Mantel test. See the scikit-bio docs for | |
| 65 more details about the Mantel test: http://scikit- | |
| 66 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html | |
| 67 | |
| 68 Parameters | |
| 69 ---------- | |
| 70 dm1 : DistanceMatrix | |
| 71 Matrix of distances between pairs of samples. | |
| 72 dm2 : DistanceMatrix | |
| 73 Matrix of distances between pairs of samples. | |
| 74 method : Str % Choices('spearman', 'pearson'), optional | |
| 75 The correlation test to be applied in the Mantel test. | |
| 76 permutations : Int % Range(0, None), optional | |
| 77 The number of permutations to be run when computing p-values. Supplying | |
| 78 a value of zero will disable permutation testing and p-values will not | |
| 79 be calculated (this results in *much* quicker execution time if | |
| 80 p-values are not desired). | |
| 81 intersect_ids : Bool, optional | |
| 82 If supplied, IDs that are not found in both distance matrices will be | |
| 83 discarded before applying the Mantel test. Default behavior is to error | |
| 84 on any mismatched IDs. | |
| 85 label1 : Str, optional | |
| 86 Label for `dm1` in the output visualization. | |
| 87 label2 : Str, optional | |
| 88 Label for `dm2` in the output visualization. | |
| 89 | |
| 90 Returns | |
| 91 ------- | |
| 92 visualization : Visualization | |
| 93 ]]></help> | |
| 94 <macros> | |
| 95 <import>qiime_citation.xml</import> | |
| 96 </macros> | |
| 97 <expand macro="qiime_citation"/> | |
| 98 </tool> |